PDBsum entry: 1nio

Hydrolase

PDB id: 1nio

Contents

Protein chain

247 a.a. *

Ligands

NAG ×3

Waters ×128

* Residue conservation analysis

PDB id:

1nio

Name:

Hydrolase

Title:

Crystal structure of beta-luffin, a ribosome inactivating pr 2.0a resolution

Structure:

B-luffin. Chain: a. Fragment: residues 1-247. Synonym: beta-luffin. Engineered: yes

Source:

Luffa aegyptiaca. Smooth loofah. Organism_taxid: 3670. Expressed in: escherichia coli. Expression_system_taxid: 562

Resolution:

2.00Å R-factor: 0.162 R-free: 0.203

Authors:

S.Wu

Key ref:

Q.J.Ma et al. (2003). Crystal structure of beta-luffin, a ribosome-inactivating protein, at 2.0 A resolution. Acta Crystallogr D Biol Crystallogr, 59, 1366-1370. PubMed id: 12876337 DOI: 10.1107/S0907444903011156

Date:

24-Dec-02 Release date: 05-Aug-03

Protein chain

P22851  (RIPB_LUFCY) -  Ribosome-inactivating protein luffin-B

Seq: 250 a.a.

Struc: 247 a.a.*

* PDB and UniProt seqs differ at 20 residue positions (black crosses)

Enzyme reactions

• Enzyme class: E.C.3.2.2.22 - rRNA N-glycosylase.
• Reaction: Endohydrolysis of the N-glycosidic bond at one specific adenosine on the 28S rRNA.

 Gene Ontology (GO) functional annotation 

• Biological process: defense response (3 terms)
• Biochemical function: hydrolase activity (2 terms)

DOI no: 10.1107/S0907444903011156

Acta Crystallogr D Biol Crystallogr 59:1366-1370 (2003)

PubMed id: 12876337

Crystal structure of beta-luffin, a ribosome-inactivating protein, at 2.0 A resolution.

Q.J.Ma, J.H.Li, H.G.Li, S.Wu, Y.C.Dong.

ABSTRACT

The crystal structure of beta-luffin at 2.0 A resolution was solved by the molecular-replacement method using polyalanyl trichosanthin as the search model. The structure was refined with CNS1.1, giving R(work) = 0.162 and R(free) = 0.204. The r.m.s.d.s of the bond lengths and bond angles are 0.008 A and 1.3 degrees, respectively. The overall structure is similar to those of other type I RIPs. Three N-acetylglucosamine (Nag) molecules are linked to residues Asn2, Asn78 and Asn85 of the protein.

Selected figure(s)

Figure 1.
Figure 1 Stereo diagram of the 2F[o] - F[c] electron-density map around the six-stranded -sheet contoured at 1.0 . (All figures were prepared with MOLSCRIPT and Raster3D).

Figure 4.
Figure 4 Stereo diagram of the simulated-annealing omit 2F[o] - F[c] electron-density map of three Nags contoured at 2 . (a) Nag248 linked to Asn2; (b) Nag249 linked to Asn78; (c) Nag250 linked to Asn85.

The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (2003, 59, 1366-1370) copyright 2003.

Figures were selected by an automated process.